the PCIe interface is not activated in the DeviceTree so if you want to use PCIe you have to activate the driver and activate the device in the DeviceTree. To activate the Device navigate to the DeviceTree file armstonea9qdl.dtsi its in the kernel arch/arm/boot/dts. Then go to the node pcie and uncomment it. Recompile the DeviceTree and try it again.

PCI Express is used very rarely in the embedded field. Most interfaces are directly available by the SOC.
For which field of application do you need it?
We gonna test PCI Express interface - Linux 4.1 combination and give a feedback.

Is the 1.5V voltage used by the module? We found out that there are some armStoneA9r2 from the first production batch where the voltage regulator is not working.
See de.wikipedia.org/wiki/PCI_Express_Mini_Card for the connector pinout. If there is no voltage on the 1.5V pins you can send us the boards for repair with RMA.

Thank you for this tip. The GPS receiver does not use 1.5V as far as I can see.

Our armStoneA9r2 does not provide 1.5V on the PCIe socket, but I guess that this is not the problem here. I will wait for you to test the PCIe interface and provide me with the correct kernel and device tree configuration.

Does the module use the PCIe interface or the USB interface? The miniPCIe connector has both signals.
The NEO-7 module from u-blox used on the EWM-G108H has UART/USB/SPI/I2C interfaces so I think USB is used.
For PCIe a separate chip has to be used to convert it to one of the interfaces of the NEO-7, but I don't think this is used.
Also on the pictures of the EWM-G108H you can see that the PCIe signals are not connected.
So you have to look for an USB device.

Thank you! I knew about the USB interface, but I was so caught up in the PCI error message that I did not think about trying USB. I had to enable USB_ACM in the kernel (USB Modem (CDC ACM) support) and then I got the /dev/ttyACM0 device as expected.